Choosing a Species
# original species data
obs_csv <- file.path(dir_data, "obs.csv")
obs_geo <- file.path(dir_data, "obs.geojson")
redo <- FALSE
# cleaned species data
obs_clean <- file.path(dir_data, "obs_clean.csv")
obs_clean_geo <- file.path(dir_data, "obs_clean.geojson")
# get species occurrence data from GBIF with coordinates
(res <- spocc::occ(
limit = 10000,
query = 'Betula lenta',
from = 'gbif', has_coords = T))
## Searched: gbif
## Occurrences - Found: 2,667, Returned: 2,667
## Search type: Scientific
## gbif: Betula lenta (2667)
# extract data frame from result
betula_df <- res$gbif$data[[1]]
count <- nrow(betula_df) # number of rows
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# convert to points of observation from lon/lat columns in data frame
obs <- betula_df %>%
sf::st_as_sf(
coords = c("longitude", "latitude"),
crs = st_crs(4326)) %>%
select(1,27:80,163)
# create .csv and sf object
readr::write_csv(betula_df, obs_csv)
sf::write_sf(obs, obs_geo)
## Warning in CPL_write_ogr(obj, dsn, layer, driver,
## as.character(dataset_options), : GDAL Error 6: DeleteLayer() not supported by
## this dataset.
# show points on map
mapview::mapview(obs, map.types = "OpenTopoMap")